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Future of Food

Study of Hunter-Gatherers' Guts Reveals Ancient Microbes

Bacteria found in far-flung indigenous groups are absent in industrialized populations.

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The Matsés people of Peru are among the last of the world’s hunter-gatherers, living on a diet composed largely of tubers and plantains.


After traveling upriver in the Peruvian Amazon, researchers from the University of Oklahoma and Peru’s National Health Institute returned with evidence that—when it comes to the bacteria living in your gut, at least—you are what you eat, not where you live.

The goal of the three-day mission was to better understand how diet and lifestyle shape the billions of bacteria living in our guts—a complex world known as the gut microbiome.

This vast community of microbes plays an active role in digestion and metabolism, with important implications for health, including susceptibility to obesity, diabetes, colon cancer, and other afflictions. (Learn more about the microbiome in National Geographic magazine's "Small, Small World."

In a paper published this week in the journal Nature Communications, University of Oklahoma geneticist Cecil Lewis and his colleagues analyzed the bacteria they collected from the digestive tracts of Amazonian hunter-gatherers called the Matsés. Among the last of the world’s hunter-gatherers, the Matsés subsist on a diet of tubers and plantains, supplemented with protein from fish, monkey, sloth, alligator, and other jungle species.

The researchers found the bacteria in the guts of these native communities included species that people in the industrialized world lack.

The team had also gathered samples from traditional potato farmers in Tunapuco, a village in the highlands of Peru’s Andes mountains. The two groups’ microbiomes were then compared to the microbiomes of residents of Norman, Oklahoma.

Rather than sharing gut bacteria species with their neighbors in Tunapuco, the Matsés hunter-gatherers had gut microbiota that matched those of other hunter-gatherers in Africa, an ocean away. But the microbial communities of the two traditional Peruvian groups resembled each other more than that of the Oklahomans, who ate a typical “industrialized diet.”

The researchers also found more diverse types of bacteria living in the guts of people in traditional societies. “It’s not about geographic distance; it’s about dietary practices,” says Lewis.

Missing Bacteria

On their journey up the Galvez River in the Amazon, Lewis’s team brought along microscopes to first teach the Matsés about microbes before asking them for fecal samples, which were then stored in a massive block of ice for the journey back to the Peruvian capital of Lima. There they were frozen and shipped to the U.S.

When they analyzed the samples back in their lab in Oklahoma, the researchers found the bacteria in the guts of these native communities included species that people in the industrialized world lack. Treponema, a bacterial genus that includes species that cause diseases like syphilis and yaws, were present in large numbers in both traditional communities.

The treponeme species in the Matsés and the farmers from Tunapuco were more closely related to variants that help break down fiber and digest carbohydrates in swine, cattle, and termites. “They’re good fermenters of fibrous material,” says Lewis.

In earlier research on the gut microbiome, conducted mostly in affluent Western populations, these treponemes didn’t show up at all. When they were first found to be common in the microbiomes of traditional peoples in Africa and South America, researchers assumed these indigenous groups were the exception to the rule.

As traditional peoples come into contact with industrialized society and change their lifestyle and diet, their gut microbiomes may be endangered.

But the new study supports other recently published research suggesting that it’s the industrialized lifestyle typified by the Oklahomans—a diet of processed food, combined with modern sanitation and frequent use of antibiotics—that is the real outlier. In 2012, Lewis’s lab sequenced 1,000-year-old fossilized feces, called coprolites, and found communities of microbes that resembled those of traditional peoples like the Matsés and the Tunapuco villagers more than those of people who eat a modern, Western diet.

“There’s nothing that stands out more than these treponemes,” Lewis says. “They’re clearly common in all traditional diets.”

In a paper published last year, Stephanie Schnorr, a researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, analyzed the gut microbiome of Hadza hunter-gatherers in Tanzania.

What Schnorr saw closely resembles what Lewis reports finding in the Matsés of Peru—including abundant treponemes and other ancient species rarely found in the industrialized world. The new study “really vindicates our findings,” says Schnorr, who was not involved with the research. “Once you start putting it all together, treponemes are popping up all over. We’re realizing that not having treponemes is probably the aberrant thing.”

Studies like these may capture a dietary portrait of preindustrial humankind before it vanishes. As traditional peoples come into contact with industrialized society and change their lifestyle and diet, their gut microbiomes may be endangered.

Lewis says that since fecal samples were first collected from the Matsés hunter-gatherers in 2012, the remote tribe “has had much more interaction with industrialized foods,” Lewis says. “We might be seeing a moment where this lifestyle is disappearing. If these traditional practices end, it may be that these treponemes are lost to us.”

Whether the presence of the treponemes—or their absence—can shed light on so-called diseases of civilization, like obesity and diabetes, remains to be seen. “These bacteria co-evolved with primates for millions of years, and now they’re gone in industrialized people,” Lewis says. “Why are they absent, and does that matter?”

Follow Andrew Curry on Twitter.

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